It's not an incompatiblity between PCI and PCIe systems but rather the difference in power between an HD1 PCIe and an HD1 PCI single core card system.
I'm not a tech or an engineer, so I can't give you a definitive answer, but I would assume that it is related to a couple of things, and the document is probably referring to this first one...
1 - In some cases, a larger session with higher track count might be created on a PCIe HD1 system, where the PCI HD1 system might not be able to open as many tracks (an HD2 PCI system might be required to handle the larger session)...
Quote:
Power Differences Relate to System Size
Technically speaking, there are more “MIPs” (millions of instructions per second)
available on the new HD PCIe card than the HD Core for PCI, though the increase in
power experienced by the user depends upon individual plug-in efficiencies. Users of HD
1 for PCIe may see a significant performance gain versus HD 1 for PCI systems,
particularly if they tend to use many instances of just a few different plug-ins and if those
plug-ins have been optimized for Pro Tools 7. However, with HD 2 and HD 3, there is a
much smaller difference in power between the systems. In fact, with systems larger than
HD 3, there is no advantage to running on PCIe versus PCI other than slot-type
compatibility.
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2 - While you can have a session on a PCIe HD1 system with Accel-only plug-ins, the PCI HD1 system would not be able to use Accel plug-ins.